scholarly journals Diversity of The Ornate Lorikeet (Trichoglossus ornatus) Birds Based on Mitochondrial DNA Protein Coding Gene

2018 ◽  
Vol 10 (2) ◽  
pp. 465-471
Author(s):  
Dwi Astuti ◽  
Siti Nuramaliati Prijono
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Gene Diversity ◽  
Haplotype Diversity ◽  
Base Pairs ◽  
Protein Coding ◽  
Dna Sequence Data ◽  
Breeding Management ◽  
Nd2 Gene

Ornate lorikeet (Trichoglossus ornatus) is an endemic bird in Sulawesi. Endemism is one of the factors in declining bird’s population. In the case of the birds conservation programme, information about gene diversity is important for basic strategy. Mitochondrial DNA of animals consists of protein coding genes including ND2 gene. This study informs diversity of the Ornate Lorikeet (Trichoglossus ornatus) birds based on DNA sequences of ND2 gene. DNA total was extracted from blood samples of 21 birds. PCR (Polymerase Chain Reaction) was performed and successfully amplified a single DNA fragment of ND2 gene for all birds. DNA fragments were sequenced and totally 997 base pairs were analyzed. NJ tree was constructed using MEGA5. All DNA sequence data showed that between the birds there were 20  polymorphic (segregating) sites with mean genetic distance was 0.004 ± 0.002 (ranged from 0,000 – 0,008), and had 17 sequence haplotypes (HTor1- HTo17). Haplotype diversity (Hd) was 0.967 ± 0.30387 and nucleotide diversity (Pi) was 0.00439 ± 0.0012. Genetic diversity information could be potential relevance to the breeding management for conservation of the birds.

scholarly journals Relationships of Tarentola (Reptilia: Gekkonidae) from the Cape Verde Islands estimated from DNA sequence data

2002 ◽  
Vol 23 (1) ◽  
pp. 47-54 ◽  
Author(s):  
António Brehm ◽  
José Jesus ◽  
D. James Harris
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Mitochondrial Genes ◽  
Cape Verde ◽  
12S Rrna ◽  
Base Pairs ◽  
Cape Verde Islands ◽  
Dna Sequence Data

AbstractThirteen specimens of Tarentola from the Cape Verde islands were sequenced for 695 base pairs of 12S rRNA and cytochrome b mitochondrial genes, and analysed with published sequences. Our results support many of the relationships previously proposed. We report the presence of Tarentola gigas Bocage, 1875 on São Nicolau and Tarentola caboverdiana nicolauensis Schleich, 1984 on São Vicente. This increases the number of genetically distinct forms on these islands; hence community structure appears to be more complex than previously understood. We also sequenced seven individuals for 375 base pairs of the nuclear gene, C-mos. Two sites were variable, much less than expected given the high levels of differentiation based on mitochondrial DNA sequences.

scholarly journals Phylogenetic Position and Generic Placement of The Socorro Wren (Thryomanes Sissonii)

The Auk ◽  
2005 ◽  
Vol 122 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Juan E. Martínez Gómez ◽  
Brian R. Barber ◽  
A. Townsend Peterson
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Species Complex ◽  
Taxonomic Classification ◽  
Phylogenetic Position ◽  
Base Pairs ◽  
House Wren ◽  
Taxonomic History ◽  
Socorro Island ◽  
Nd2 Gene

Abstract Since early in its taxonomic history, placement of the Socorro Wren (Thryomanes sissonii) has been an object of contention. Of particular interest is its current placement in the genus Thryomanes, which makes that genus ditypic and leads to an odd biogeographic scenario for the Socorro Wren's colonization of Socorro Island. We assessed its phylogenetic position by analyzing 516 base pairs of mitochondrial DNA sequences from the ND2 gene of this species and 14 additional wren taxa. Contrary to its present placement, the Socorro Wren is nested phylogenetically within the House Wren species complex, being placed as sister to the clade Troglodytes aedon + T. musculus. The current hypothesis (i.e. sister to Thryomanes bewickii) is strongly invalidated by our analysis. Our analyses indicate that the most appropriate taxonomic classification for the Socorro Wren is Troglodytes sissonii. Posición Filogenética y Ubicación Genérica de Thryomanes sissonii

scholarly journals A Multifaceted Approach to the Characterization of an Intergeneric Hybrid Manakin (Pipridae) from Brazil

The Auk ◽  
2002 ◽  
Vol 119 (4) ◽  
pp. 1114-1120 ◽  
Author(s):  
Miguel  Marini ◽  
Shannon J. Hackett
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Female Parent ◽  
Intergeneric Hybrid ◽  
Morphological Characters ◽  
Multifaceted Approach ◽  
Dna Sequence Data ◽  
Nd2 Gene

Abstract A new intergeneric hybrid manakin is characterized using morphological characters and mitochondrial and nuclear DNA sequences. Many morphological traits suggest the bird is intermediate between Ilicura militaris and Chiroxiphia caudata. Sequences of the maternally inherited mitochondrial ND2 gene demonstrate the female parent to be Chiroxiphia caudata, and the nuclear beta-fibrinogen intron 5 sequences can not eliminate Chiroxiphia and Ilicura as parents. Therefore, DNA sequence data lead to the conclusion that Ilicura is the male parent of this unusual bird. This study is important because it highlights the significance of using multiple character systems in diagnosing unusual bird specimens.

Phylogeny-based species delimitation of southern Philippines bent-toed geckos and a new species of Cyrtodactylus (Squamata: Gekkonidae) from western Mindanao and the Sulu Archipelago

Zootaxa ◽  
2010 ◽  
Vol 2390 (1) ◽  
pp. 49 ◽  
Author(s):  
LUKE J. WELTON ◽  
CAMERON D. SILER ◽  
ARVIN C. DIESMOS ◽  
RAFE M. BROWN
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Dna Sequences ◽  
Sequence Data ◽  
Color Pattern ◽  
Reciprocal Monophyly ◽  
Dna Sequence Data ◽  
Natural Park ◽  
Gallery Forests ◽  
A New Species

Using a combination of fixed morphological character differences, mitochondrial DNA sequence data, and an estimate of phylogeny as our guide, we describe a new species of bent-toed gekkonid lizard (Genus: Cyrtodactylus) from southwestern Mindanao Island, and northeastern portions of the Sulu Archipelago, southern Philippines. The new species resembles C. annulatus, but differs from this and all other congeners by characteristics of external morphology, color pattern, and body size. In addition, the new species is distinguished from congeners by marked genetic divergence and reciprocal monophyly of mitochondrial DNA sequences. The new species is common in pristine, low elevation gallery forests throughout Pasonanca Natural Park, Zamboanga Peninsula, southwestern Mindanao Island, and the northeastern portions of the Sulu Archipelago.

scholarly journals Hierarchical Models for Mitochondrial DNA Sequence Data

2016 ◽  
Vol 36 (1) ◽  
Author(s):  
Paola Berchialla
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Population History ◽  
Parametric Models ◽  
Italian Population ◽  
Bayesian Hierarchical ◽  
Dna Sequence Data ◽  
Mitochondrial Dna Sequence

We introduce a Bayesian hierarchical model for mitochondrial DNA sequence data, which is fitted via acceptance-rejection algorithms. The model incorporates parametric models of population history explicitly as well as a mutational process allowing for a simultaneous parameter estimation whose importance has become increasingly clear in many recent studies. The model is applied to a sample of DNA sequences from the Italian population.

scholarly journals Two new species of Verruconis from Hainan, China

MycoKeys ◽  
2019 ◽  
Vol 48 ◽  
pp. 41-53 ◽  
Author(s):  
Min Qiao ◽  
Weiguang Tian ◽  
Rafael F. Castañeda-Ruiz ◽  
JianPing Xu ◽  
Zefen Yu
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Sequence Data ◽  
Nuclear Ribosomal Dna ◽  
Closely Related Species ◽  
Protein Coding ◽  
Dna Sequence Data ◽  
Protein Coding Genes ◽  
Two New Species ◽  
New Perspective

Two new species of the genusVerruconis,V.hainanensisandV.pseudotricladiata, were described using combined morphological and DNA sequence data. The DNA sequences of respective strains including nuclear ribosomal DNA genes (nuSSU, ITS, nuLSU) and fragments of three protein-coding genes (ACT1, BT2, TEF1) were sequenced and compared with those from closely-related species to generaOchroconisandVerruconis(Family Sympoventuriaceae, Order Venturiales). Morphologically, both species showed typical ampulliform conidiophores and conidiogenous cells, features not seen in other species ofVerruconis. The conidia ofV.hainanensisare fusiform and those ofV.pseudotricladiataare Y or T shaped, similar to old members of a closely-related genusScolecobasidium. The addition of these two new species provides a new perspective on the heterogeneity ofScolecobasidium.

scholarly journals Is there evidence of selection in the dopamine receptor D4 gene in Australian invasive starling populations?

2015 ◽  
Vol 61 (3) ◽  
pp. 505-519 ◽  
Author(s):  
Lee Ann Rollins ◽  
Michael R. Whitehead ◽  
Andrew P. Woolnough ◽  
Ron Sinclair ◽  
William B. Sherwin
Keyword(s):  
Mitochondrial Dna ◽  
Dopamine Receptor ◽  
Dna Sequence ◽  
Population Differentiation ◽  
Sequence Data ◽  
Gene Diversity ◽  
Novelty Seeking ◽  
Dna Sequence Data ◽  
Mitochondrial Dna Sequence ◽  
Dopamine Receptor D4

Abstract Although population genetic theory is largely based on the premise that loci under study are selectively neutral, it has been acknowledged that the study of DNA sequence data under the influence of selection can be useful. In some circumstances, these loci show increased population differentiation and gene diversity. Highly polymorphic loci may be especially useful when studying populations having low levels of diversity overall, such as is often the case with threatened or newly established invasive populations. Using common starlings Sturnus vulgaris sampled from invasive Australian populations, we investigated sequence data of the dopamine receptor D4 gene (DRD4), a locus suspected to be under selection for novelty-seeking behaviour in a range of taxa including humans and passerine birds. We hypothesised that such behaviour may be advantageous when species encounter novel environments, such as during invasion. In addition to analyses to detect the presence of selection, we also estimated population differentiation and gene diversity using DRD4 data and compared these estimates to those from microsatellite and mitochondrial DNA sequence data, using the same individuals. We found little evidence for selection on DRD4 in starlings. However, we did find elevated levels of within-population gene diversity when compared to microsatellites and mitochondrial DNA sequence, as well as a greater degree of population differentiation. We suggest that sequence data from putatively nonneutral loci are a useful addition to studies of invasive populations, where low genetic variability is expected.

scholarly journals A new Indian species of Rhinophis Hemprich, 1820 closely related to R. sanguineus Beddome, 1863 (Serpentes: Uropeltidae)

Zootaxa ◽  
2020 ◽  
Vol 4881 (1) ◽  
pp. 1-24
Author(s):  
FILIPA L. SAMPAIO ◽  
SURYA NARAYANAN ◽  
VIVEK PHILIP CYRIAC ◽  
GOVINDAPPA VENU ◽  
DAVID J. GOWER
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Dna Sequences ◽  
Sequence Data ◽  
Colour Pattern ◽  
Indian Species ◽  
Peninsular India ◽  
Dna Sequence Data ◽  
New Species Description ◽  
The Western Ghats

A new species of the uropeltid (shieldtail snake) genus Rhinophis is described based on a type series of seven specimens from the Wayanad region of the Western Ghats of peninsular India. The holotype was collected before 1880 but had been misidentified as the phenotypically similar and parapatric (possibly partly sympatric) R. sanguineus. Rhinophis karinthandani sp. nov. is diagnosed by a combination of 15 dorsal scale rows at midbody, 4–8 pairs of subcaudal scales, colour pattern (uniformly dark above, whitish below with extensive dark mottling), and by its distinct mitochondrial DNA sequences (e.g. >7.6% uncorrected p-distance for nd4). Phylogenetic analysis of mitochondrial DNA sequence data indicates that the new species is most closely related to R. sanguineus among currently recognised species, with this pair most closely related to the partly sympatric R. melanoleucus. The new species description brings the number of currently recognised species in the genus to 24, six of which are endemic to India and 18 endemic to Sri Lanka. A new key to the identification of Indian species of Rhinophis is provided.

scholarly journals Algoritma Needleman-Wunsch dalam Menentukan Tingkat Kemiripan Urutan DNA Rusa Timor (Cervus timorensis) dan Rusa Merah (Cervus elaphus)

2020 ◽  
Vol 3 (2) ◽  
pp. 125
Author(s):  
Hibban Kholiq ◽  
Mamika Ujianita Romdhini ◽  
Marliadi Susanto
Keyword(s):  
Dna Sequence ◽  
Sequence Alignment ◽  
Cervus Elaphus ◽  
Dna Sequences ◽  
Sequence Data ◽  
Local Alignment ◽  
Base Pairs ◽  
European Continent ◽  
Dna Sequence Data ◽  
Search Tool

Sequence alignment is a basic method in sequence analysis. This method is used to determine the similaritiy level of DNA sequences. The Needleman-Wunsch algorithm is an algorithm that can be used to solve the problem of sequence alignment. This research shows that the relation T (i, j) used in the Needleman-Wunsch algorithm is a function where T: (ℕ0 ℕ0) → ℤ. The function T (i, j) is a recursive function. Moreover, DNA sequence data used are DNA sequences from the Timor Deer, which are the identities of the provinces of West Nusa Tenggara and Red Deer, which are typical deer from the European continent as a comparison. The DNA sequence data was obtained from BLAST (Basic Local Alignment Search Tool). Based on the alignment, the most optimal alignment is obtained by forming 666 base pairs sequences with 322 matches, 230 missmatches and 114 gaps, meaning that the two DNA sequences have a 48% similarity (322/666).

A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia

Zootaxa ◽  
2020 ◽  
Vol 4766 (3) ◽  
pp. 472-484
Author(s):  
HANNAH E. SOM ◽  
L. LEE GRISMER ◽  
PERRY L. JR. WOOD ◽  
EVAN S. H. QUAH ◽  
RAFE M. BROWN ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Dna Sequence ◽  
Rare Species ◽  
Sequence Data ◽  
Peninsular Malaysia ◽  
Tropical Asia ◽  
Dna Sequence Data ◽  
A New Species ◽  
Lines Of Evidence

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12. 

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